Not sure how accurate the title is but its best I could think of. From the attached pictures are the solid model, the models curves in ICEM along with the model blocked and meshed and what the mesh looks like in CFX Pre.

I have been following the 3D pipe junction tutorial as the geometry is similar and my problems start when I start removing blocks to give me the hollow sections. The model I've made is of the fluid, in this case air of a gamma type Stirling engine, the hollowed section is the displacer piston which will move in the analysis.

I'm looking at splitting the model up into different sections and mesh them individually but I am not sure whether to then merge he meshes within ICEM or within CFX Pre.

I'm using ICEM so I could take advantage of the replay feature to re-mesh the model when distortion reaches a set value as I have tried CFX Mesh in workbench to create the mesh but after a couple of time steps I get a negative volume error due to the predominance of tet elements.

If anyone has any tips, pointers or alternatives on how to get a suitable mesh to perform a analysis with the pistons moving it would be greatly appreciated.

Your last image seems to show the blocking, but it is not a good topology at all...

Just looking at the cylinder on the right... What you really have are three cylinders...

1) The outer wall

2) The chamber wall

3) the valve

Just imagine these extended from end to end. That is how you should block it. One Ogrid (CGrid since it is a symmetry model) that has its central HGrid within the valve stem. Then split the Ogrid twice (Once for the valve diameter and once for the piston diameter). Split along the cylinder for the piston face... Make all your associations and delete the blocks that are not part of your fluid volume...

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However when starting solver it exits with return code 1 and just before i get a notice about the heat transfer coefficient uses wall adjacent temperature for bulk temperature but no error code or other message indicating whats wrong.

I've changed a few of the boundary conditons within pre but i'm now out of ideas.